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1 a.nocvrt Test that Matrix eQTL gives correct estimates for additive linear model. Homoscedastic case without covariates.
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2 b.cvrt Test that Matrix eQTL gives correct estimates for additive linear model. Homoscedastic case with covariates.
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3 c.weights Test that Matrix eQTL gives correct estimates for additive linear model. Heteroscedastic case with covariates.
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4 d.ANOVA Test that Matrix eQTL gives correct estimates for ANOVA linear model with 3 groups. Heteroscedastic case with covariates.
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5 d.ANOVA5 Test that Matrix eQTL gives correct estimates for ANOVA linear model with 5 groups. Heteroscedastic case with covariates.
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6 e.interaction Test that Matrix eQTL gives correct estimates for linear model with genotype-covariate interaction. Heteroscedastic case with covariates.
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7 p.hist Sample code for plotting histogram of p-values
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8 q.qqplot Sample code for plotting QQ-plot of p-values
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9 sample.all Sample code for eQTL analysis of the toy data set.
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10 sample.cis Sample code for eQTL analysis of the toy data set with separate p-value thresholds and FDR estimation for cis- and trans-eQTLs.
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